Contacts of the helix formed by residues 2010 - 2018 (chain E) in PDB entry 3NBN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY2010 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1975E GLN* 4.6 6.1 - - - -
2008E VAL 3.9 1.2 + - - -
2009E GLU* 1.3 69.6 - - - +
2011E MET* 1.3 63.3 + - - -
2012E LEU* 3.3 3.1 - - - +
2013E GLU* 2.8 24.9 + - - +
2014E ASP* 3.1 19.1 + - - +
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Residues in contact with MET2011 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969E ALA 4.2 1.3 - - - +
1970E VAL* 4.0 24.0 - - + +
1973E ASP* 3.1 51.6 - - - +
1974E ALA 3.7 4.7 - - - +
1975E GLN* 4.4 10.8 + - - +
1978E PHE* 3.6 48.2 - - + -
2003E ALA* 4.7 6.1 - - + -
2008E VAL* 3.6 19.3 - - + -
2009E GLU 2.7 18.3 + - - +
2010E GLY* 1.3 68.3 - - - -
2012E LEU* 1.3 65.6 + - - +
2014E ASP 3.1 1.4 + - - +
2015E LEU* 2.9 29.7 + - + +
22F ARG* 4.0 4.7 - - - +
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Residues in contact with LEU2012 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2000E LEU* 3.6 33.2 - - + +
2003E ALA* 4.0 19.5 - - + +
2004E ALA* 4.0 12.1 - - + +
2008E VAL* 5.0 5.6 + - - +
2010E GLY 3.0 3.3 + - - +
2011E MET* 1.3 76.7 - - - +
2013E GLU* 1.3 58.7 + - + +
2015E LEU* 3.4 2.9 + - - +
2016E ILE* 2.9 34.9 + - + +
2044E ALA* 3.6 25.8 - - + +
2047E VAL* 4.1 17.9 - - + -
2048E LEU* 3.5 33.4 - - + -
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Residues in contact with GLU2013 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2010E GLY* 2.8 17.6 + - - +
2012E LEU* 1.3 76.7 - - + +
2014E ASP* 1.3 62.9 + - - +
2016E ILE* 2.9 9.9 + - - +
2017E ASN* 2.8 51.4 + - - +
2047E VAL* 3.8 35.7 - - + +
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Residues in contact with ASP2014 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975E GLN* 3.2 17.0 + - - -
1978E PHE* 4.1 4.0 - - + -
1979E GLN* 3.0 21.6 - - - +
1982E ILE* 3.4 17.7 - - + +
2010E GLY* 3.1 16.8 + - - +
2011E MET 3.1 4.9 + - - +
2013E GLU* 1.3 79.0 - - - +
2015E LEU* 1.3 59.1 + - - +
2017E ASN* 3.8 10.6 + - - +
2018E SER* 2.9 33.6 + - - -
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Residues in contact with LEU2015 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966E LEU* 4.4 19.3 - - + -
1970E VAL* 4.9 1.8 - - + -
1978E PHE* 3.9 26.5 - - + -
1982E ILE* 4.3 7.6 - - + -
1989E LEU* 4.4 23.0 - - + +
1999E PRO* 3.8 13.9 - - + +
2000E LEU* 3.6 43.1 - - + +
2003E ALA* 4.4 5.4 - - + -
2011E MET* 2.9 18.3 + - + +
2012E LEU 3.6 3.1 - - - +
2014E ASP* 1.3 74.7 - - - +
2016E ILE* 1.3 67.9 + - - +
2018E SER* 3.2 11.2 + - - -
2019E HIS 3.3 0.3 + - - -
2020E ALA* 3.2 24.2 + - + +
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Residues in contact with ILE2016 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2000E LEU* 4.3 16.4 - - + -
2012E LEU* 2.9 23.5 + - + +
2013E GLU* 2.9 10.8 + - - +
2015E LEU* 1.3 74.6 - - - +
2017E ASN* 1.3 58.2 + - - +
2019E HIS* 2.7 31.0 + - - -
2020E ALA* 3.8 6.9 + - - +
2022E VAL* 5.1 13.4 - - + +
2047E VAL* 3.5 28.7 - - + +
2048E LEU* 4.1 26.9 - - + -
2051E ASN* 3.5 38.1 - - + +
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Residues in contact with ASN2017 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013E GLU* 2.8 41.9 + - - +
2014E ASP* 3.8 9.9 + - - +
2016E ILE* 1.3 72.7 - - - +
2018E SER* 1.3 59.3 + - - +
2019E HIS* 2.9 33.4 + - - -
2051E ASN* 5.2 3.8 + - - -
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Residues in contact with SER2018 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1985B ARG* 3.9 24.4 + - - +
1982E ILE* 3.3 23.1 + - - +
1989E LEU* 3.6 26.6 - - - +
2014E ASP 2.9 23.2 + - - -
2015E LEU 3.2 2.4 + - - -
2017E ASN* 1.3 70.7 - - - +
2019E HIS* 1.3 74.2 + - - +
2020E ALA 3.6 0.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il